ATTED-II provides coexpressed gene networks for Arabidopsis

Nucleic Acids Res. 2009 Jan;37(Database issue):D987-91. doi: 10.1093/nar/gkn807. Epub 2008 Oct 25.


ATTED-II ( is a database of gene coexpression in Arabidopsis that can be used to design a wide variety of experiments, including the prioritization of genes for functional identification or for studies of regulatory relationships. Here, we report updates of ATTED-II that focus especially on functionalities for constructing gene networks with regard to the following points: (i) introducing a new measure of gene coexpression to retrieve functionally related genes more accurately, (ii) implementing clickable maps for all gene networks for step-by-step navigation, (iii) applying Google Maps API to create a single map for a large network, (iv) including information about protein-protein interactions, (v) identifying conserved patterns of coexpression and (vi) showing and connecting KEGG pathway information to identify functional modules. With these enhanced functions for gene network representation, ATTED-II can help researchers to clarify the functional and regulatory networks of genes in Arabidopsis.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Arabidopsis / genetics*
  • Arabidopsis / metabolism
  • Databases, Genetic*
  • Gene Expression
  • Gene Expression Regulation, Plant*
  • Gene Regulatory Networks*
  • Genes, Plant
  • Protein Interaction Mapping